After giving in the summary of my thesis today, I also started writing the actual thing. Of course this is not something I will finish in a few days. It’s a long journey that will go on until I deliver it.
Aside that, I’ve been having some problems with R, a language which I really don’t like and I hope to use as less as possible. I was obtaining a list of differentially expressed genes (DEGs) out of some data files with SAM, and of course I had to supply a matrix with expression values for every gene.
What I didn’t understand is why on Earth the package siggenes understands that, but when outputting the result (command sam2excel) it’s giving the row of the file where the gene is, instead of the actual gene. If I supplied the IDs, whatever they are, they should be added as well! But you can output those only with “list.siggenes” which of course doesn’t add the d-score I need…
In general, I find R slow, clumsy and counter-intuitive. There are much better languages out there (and with better interactive shells), I can’t really understand why it is so popular among people who do bioinformatics…
Looks like my laptop doesn’t really want to keep its data in stable form. Like I have blogged previously, the bus-reset issue apparently trashed my root partition again. I do not know the cause as it seemed a normal shutdown… but the moment I rebooted I had lost a lot of files (thankfully not on /home: I’m glad I keep data separated from the rest).
Reinstalling proved less difficult, thanks to a Kubuntu DVD I burnt with my other computer. However, I still had to tinker manually because of read errors (notice that this seems to be an issue with my DVD-ROM, rather than with the DVD itself). When those were unrecoverable, I manually changed the temporary sources.list to point to Internet mirrors and all was well.
I still don’t know what causes such problems. I considered trying Gutsy Gibbon due to a new kernel, but being in alpha stage means it may get much worse bugs. I’m tempted to file a bug, but since there are a few othrs with similar issues, I have to check them first.
What’s sure is that I’ll be using partimage to make images of my drive. It’ll be much easier to restore the configuration like that.
Recently, I had to do a few scans with my old but trusty BenQ 640BU. Given that I could not use any GUI due to a long-standing Feisty bug, I tried to settle for command line scanning with the scanimage command from SANE. The main problem is that scanimage only saves images in PNM or TIFF formats. I wanted to use JPEG or PNG, but apparently that looked impossible to do.
Instead, I found that scanimage sends its results to standard output, and also that ImageMagick can accept standard input as source file, it was easy to convert on the fly:
scanimage --format pnm | convert -format png - test.png
“-” tells convert to use the standard input. Another great example of the power of the command line.
